Common hydrogen bond interactions in diverse phosphoryl transfer active sites

Citation for published article

Correlation between total air pollutant emissions and incidence of type 1 diabetes in the Russian Federation

DOI

10.1371/journal.pone.0108310

Document Type

Journal Article

Publication Date

9-19-2014

Publication Title

PLoS ONE

School

Bayer School of Natural and Environmental Sciences

Abstract

© 2014 Summerton et al. Phosphoryl transfer reactions figure prominently in energy metabolism, signaling, transport and motility. Prior detailed studies of selected systems have highlighted mechanistic features that distinguish different phosphoryl transfer enzymes. Here, a top-down approach is developed for comparing statistically the active site configurations between populations of diverse structures in the Protein Data Bank, and it reveals patterns of hydrogen bonding that transcend enzyme families. Through analysis of large samples of structures, insights are drawn at a level of detail exceeding the experimental precision of an individual structure. In phosphagen kinases, for example, hydrogen bonds with the O3b of the nucleotide substrate are revealed as analogous to those in unrelated G proteins. In G proteins and other enzymes, interactions with O3b have been understood in terms of electrostatic favoring of the transition state. Ground state quantum mechanical calculations on model compounds show that the active site interactions highlighted in our database analysis can affect substrate phosphate charge and bond length, in ways that are consistent with prior experimental observations, by modulating hyperconjugative orbital interactions that weaken the scissile bond. Testing experimentally the inference about the importance of O3βinteractions in phosphagen kinases, mutation of arginine kinase Arg280decreases kcat, as predicted, with little impact upon KM.Copyright:

Link to Full Text

Share

COinS